no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 4. August 2015 20:43:47 Betreff: Re: [Freesurfer] cannot find qdec file oops, sorry for the delay, thanks for the reminder. The problem is that you have a blank line at the end of your long.qdec.table.dat file. Remove the line and see if it works. doug On 08/04/2015 12:42 PM, Clara Kühn wrote: > Hi Doug, > did the fordoug.log file give any information about why FreeSurfer can't find > my qdec file? > > Cheers and thanks for working on this! > Clara > > ----- Ursprüngliche Mail ----- > Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Montag, 3. August 2015 17:16:18 > Betreff: Re: [Freesurfer] cannot find qdec file > > can you run > > mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat > --target 7kids_template_sc1 --hemi lh --meas thickness --out > /scr/etsch2/kids/ct/qdec/lh.thickness.mgh |& tee fordoug.log > > and send me fordoug.log ? > > > On 8/3/15 10:38 AM, Clara Kühn wrote: > > > > the command line is this: > mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat > --target 7kids_template_sc1 --hemi lh --meas thickness --out > /scr/etsch2/kids/ct/qdec/lh.thickness.mgh > > the terminal output is this: > nsubjects = 22 > ERROR: cannot find /scr/etsch2/kids/ct/.long. > > and the actual qdec file is attached. > Cheers, Clara > > ----- Ursprüngliche Mail ----- > Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An: > freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 > Betreff: Re: [Freesurfer] cannot find qdec file > > Can you send your command line, full terminal output, and your > long.qdec.table.dat file? > > On 8/3/15 10:31 AM, Clara Kühn wrote: > > > > ok, it can only access the file if I type > ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) > > but if I then use that path for the mris_preproc command I get > nsubjects = 22 > ERROR: cannot find /scr/etsch2/kids/ct/.long. > > > > ----- Ursprüngliche Mail ----- > Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An: > freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 > Betreff: Re: [Freesurfer] cannot find qdec file > > that is probably not the full path. Try typing > > ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat > > If it says it cannot find the file, then it is not the full path. Maybe > you need a forward slash (ie, "/") in the beginning? > > On 8/3/15 10:18 AM, Clara Kühn wrote: > > > > then I get the error ERROR: cannot find > scr/etsch2/kids/ct/qdec/long.qdec.table.dat > > I had tried that. Sorry, no luck with that. > > ----- Ursprüngliche Mail ----- > Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An: > freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 > Betreff: Re: [Freesurfer] cannot find qdec file > > you have to give it the entire path to the file > > On 8/3/15 10:14 AM, Clara Kühn wrote: > > > > Dear FS-experts, > > I want to analyze my longitudinal data with your suggested LME models and am > therefore following the walkthrough by J. Bernal. I get an error though very > early on when using the command > mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 > --hemi lh --meas thickness --out qdec/lh.thickness.mgh > > It always says > ERROR: cannot find qdec/long.qdec.table.dat > > Yes, the walkthrough asks for an input file named just qdec.table.dat, but I > haven't got that. So far in the longitudinal stream there are > long.qdec.table.dat and cross.qdec.table.dat files but no simple > qdec.table.dat files. So I figured I'd use the long.qdec file because FS > needs to get the information about the long timepoints. > But it cannot find the file, even though I see it. I've also tried copying > the long.qdec file and naming it qdec.table.dat but it still doesn't find it. > > The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat > and my SUBJECTS_DIR is scr/etsch2/kids/ct > > Can you help me see what I'm missing? > Thanks a lot in advance, > Clara > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information > in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
